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ISCN Cytogenetic Nomenclature Parser

Decodes ISCN karyotype strings into plain-language clinical descriptions

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Why use it

Helps non-geneticist physicians quickly understand complex cytogenetic reports. Breaks down each component of the ISCN string into its structural meaning.

About

A lexical analysis engine that translates standard ISCN cytogenetic nomenclature strings into plain-language descriptions for clinical interpretation and patient communication. Supports karyotype strings including translocations, inversions, deletions, duplications, isochromosomes, rings, markers, mosaicism, and sex chromosome anomalies. Accepts both preset selections and free-text input for maximum flexibility.

When to use

  • Translating a karyotype report for a patient chart or clinical summary.
  • Quickly verifying the structural components of an ISCN string.
  • Teaching cytogenetics nomenclature to trainees.
  • Preparing plain-language reports for multidisciplinary team meetings.

Formula

Regex-based lexical parsing of ISCN string components.

Pearls & pitfalls

  • The slash "/" separates different cell lines in mosaicism (e.g., 47,XX,+21/46,XX).
  • The double slash "//" denotes chimerism (two genetically distinct cell populations, e.g., 46,XX//46,XY).
  • "der" indicates a derivative chromosome resulting from a rearrangement.
  • "t(X;Y)(pA;qB)" describes a translocation between chromosomes X and Y with breakpoints at pA and qB.
  • "inv(X)(pA;qB)" describes a pericentric inversion (breaks in both arms); "inv(X)(qA;qB)" is paracentric (both breaks in same arm).
  • "+21" means an extra chromosome 21 (gain); "-X" means loss of chromosome X.
  • "ish" prefix indicates FISH confirmation; "arr" indicates microarray nomenclature.
  • Nomenclature is case-sensitive: "p" = short arm, "q" = long arm.

Next steps

Clinical correlation required for specific breakpoints. For molecular karyotypes (arr notation), additional parsing rules apply.

Evidence

ISCN 2024: An International System for Human Cytogenomic Nomenclature. S. Karger, Basel.

References

  1. ISCN 2024: An International System for Human Cytogenomic Nomenclature. McGowan-Jordan J, Hastings RJ, Moore S, eds. S. Karger, Basel.
  2. Gardner RJM, Sutherland GR, Shaffer LG. Appendix B: Cytogenetic Abbreviations and Nomenclature.